This is actually an interesting question. I have noticed that the monsters in the MM do not necessarily reflect the CR guidelines in the DMG. What I usually end up doing for higher level monsters is look at the average HPs and defenses for a monster of that CR in the DMG and adjusting as needed. Tends to work well.
I think that's partly due to the fact that the MM came out long before the DMG. Since I don't run published campaigns, I don't really hit some of the issues others hit. If I want a fight with orcs, I just throw as many orcs as I need to be a threat.
But some of the things I do are along the same lines - if I want to throw a bunch of lower level monsters at a party with significantly high AC, I'll sometime just give them a bonus to hit and possibly greater damage. Kind of like the minion idea from 4E except that it will take more than 1 HP of damage to kill the monster.
I do it because they feel like a threat while at the same time the caster can really contribute to the combat at a critical moment with those AOE spells.
It would be interesting to have a list - what do people do to increase individual monster threat level?